When you are writing content with two voices sharing the same staff, Flat put the stems of one voice upward, and the stems of the other voice are facing downward.
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Sometime the stems direction is not the more appropriate:
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We just added a tool that comes handy in this kind of situations: you can now swap the voices assigned to the selection. To do so, make a range selection, then click on the voices button. Finally, click on the Swap voice button.
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I hope this tool will make the composition process easier for you!